def fw_heudiconv_download():
"""Use fw-heudiconv to download BIDS data.
Returns True if success or False if there are no dwi files."""
subjects = [subject_container.label]
if not use_all_sessions:
# find session object origin
sessions = [session_container.label]
else:
sessions = None
# Do the download!
bids_root.parent.mkdir(parents=True, exist_ok=True)
downloads = export.gather_bids(fw, project_label, subjects, sessions)
export.download_bids(fw, downloads, str(bids_dir.resolve()), dry_run=False)
# Download the extra T1w or T2w
if extra_t1 is not None:
get_external_bids(extra_t1, extra_t1_path)
if extra_t2 is not None:
get_external_bids(extra_t2, extra_t2_path)
dwi_files = [fname for fname in bids_root.glob("**/*") if "dwi/" in str(fname)]
if not len(dwi_files):
logger.warning("No DWI files found in %s", bids_root)
return False
return True
logger.info("Dry run: {}".format(dry_run))
# action
if action == "Curate":
curate.convert_to_bids(fw,
project_label,
heuristic,
subjects,
sessions,
dry_run=dry_run)
elif action == "Export":
downloads = export.gather_bids(fw, project_label, subjects, sessions)
export.download_bids(fw, downloads, "/flywheel/v0/input", dry_run=dry_run)
if not dry_run:
pass
# tidy up
# output_dir = "/flywheel/v0/output"
# os.system("zip -r {}_BIDSexport.zip output/*".format(destination['id']))
# os.system("mv *.zip output")
# to_remove = os.listdir(output_dir)
# to_remove = ["{}/{}".format(output_dir, x) for x in to_remove if ".zip" not in x]
# for x in to_remove:
# if os.path.isfile(x):
# os.remove(x)
# else:
# shutil.rmtree(x)
subject_container = fw.get(session_container.parents['subject'])
subjects = [subject_container.label]
else:
sessions = None
subjects = None
# logging stuff
logger.info("Running fw-heudiconv with the following settings:")
logger.info("Project: {}".format(project_label))
logger.info("Subject(s): {}".format(subjects))
logger.info("Session(s): {}".format(sessions))
logger.info("Action: {}".format(action))
logger.info("Dry run: {}".format(dry_run))
# action
if action == "Curate":
print("This gear does not do BIDS Curation!")
elif action == "Export":
downloads = export.gather_bids(fw, project_label, subjects, sessions)
export.download_bids(fw, downloads, "/flywheel/v0/input", dry_run=dry_run, folders_to_download=['anat', 'func'])
if not dry_run:
pass
elif action == "Tabulate":
print("This gear does not do BIDS Tabulation!")
else:
raise Exception('Action not specified correctly!')
def fw_heudiconv_download():
"""Use fw-heudiconv to download BIDS data."""
subjects = [subject_container.label]
sessions = [session_container.label]
# Use manually specified T1 if it exists
if manual_t1 is not None:
anat_input = manual_t1_path
subject_label = subject_container.label.replace('_',
'x').replace(' ', 'x')
session_label = session_container.label.replace('_',
'x').replace(' ', 'x')
prefix = 'sub-{}_ses-{}_'.format(subject_label, session_label)
return True, anat_input, prefix
# Do the download!
bids_root.parent.mkdir(parents=True, exist_ok=True)
downloads = export.gather_bids(fw, project_label, subjects, sessions)
export.download_bids(fw,
downloads,
str(bids_dir.resolve()),
dry_run=False,
folders_to_download=['anat'])
bids.config.set_option('extension_initial_dot', True) # suppress warning
layout = bids.BIDSLayout(bids_root)
filters = {}
if bids_filter_path:
logger.info("Using {} as BIDS filter.".format(bids_filter_path))
with open(bids_filter_path) as f:
data = json.load(f)
try:
filters = data["t1w"]
except KeyError as ke:
print(ke)
logger.warning("Could not find 't1w' field in json.")
logger.info("BIDS filter file not formatted correctly.")
return False
else:
if bids_sub:
filters["subject"] = [bids_sub]
else:
filters["subject"] = subjects
if bids_ses:
filters["session"] = [bids_ses]
else:
filters["session"] = sessions
if bids_acq:
filters["acquisition"] = bids_acq
if bids_run:
filters["run"] = bids_run
anat_list = layout.get(return_type='file',
suffix='T1w',
extension=['.nii', '.nii.gz'],
**filters)
# if there are multiple files or no files, error out
# otherwise just use the one
if len(anat_list) > 1:
logger.warning(
"Multiple anatomical files found in %s. If you want to process multiple images, use the longitudinal gear.",
bids_root)
return False
elif not len(anat_list) or len(anat_list) == 0:
logger.warning("No anatomical files found in %s", bids_root)
return False
else:
anat_input = anat_list[0]
logger.info("Using {} as input anatomical image.".format(anat_input))
# Generate prefix from bids layout
basename = os.path.basename(anat_input).split('.')[0]
prefix = basename.replace('_T1w', '') + '_'
return True, anat_input, prefix
def fw_heudiconv_download():
"""Use fw-heudiconv to download BIDS data."""
subjects = [subject_container.label]
sessions = [session_container.label]
# Use manually specified T1 if it exists
if manual_t1 is not None:
anat_input = manual_t1_path
subject_label = subject_container.label.replace('_', 'x')
session_label = session_container.label.replace('_', 'x')
prefix = 'sub-{}_ses-{}_'.format(subject_label, session_label)
return True, anat_input, prefix
# Do the download!
bids_root.parent.mkdir(parents=True, exist_ok=True)
downloads = export.gather_bids(fw, project_label, subjects, sessions)
export.download_bids(fw,
downloads,
str(bids_dir.resolve()),
dry_run=False,
folders_to_download=['anat'])
layout = BIDSLayout(bids_root)
# Get subject and session label
# subject_label = layout.get(return_type='id', target='subject')[0].strip("[']")
# session_label = layout.get(return_type='id', target='session')[0].strip("[']")
filters = {}
if bids_sub:
filters["subject"] = [bids_sub]
else:
filters["subject"] = subjects
if bids_ses:
filters["session"] = [bids_ses]
else:
filters["session"] = sessions
if bids_acq:
filters["acquisition"] = bids_acq
if bids_run:
filters["run"] = bids_run
anat_list = layout.get(return_type='file',
extension=['.nii', '.nii.gz'],
**filters)
# if there are multiple files or no files, error out
# otherwise just use the one
if len(anat_list) > 1:
logger.warning(
"Multiple anatomical files found in %s. If you want to process multiple images, use the longtidunal gear.",
bids_root)
return False
elif not len(anat_list) or len(anat_list) == 0:
logger.warning("No anatomical files found in %s", bids_root)
return False
else:
anat_input = anat_list[0]
logger.info("Using {} as input anatomical image.".format(anat_input))
# Generate prefix from bids layout
basename = os.path.basename(anat_input).split('.')[0]
prefix = basename.replace('_T1w', '') + '_'
return True, anat_input, prefix